It's probably already been discussed to death, but there was something that felt very special with the beast trio being unique legendaries (at least as far as ingame lore is concerned) that tied together with the Burned Tower legend about 3 mons being revived by Ho-Oh.
Now the implication here is that they're just like any other pokemon with entire populations of them hidden in the wild. I know it's such a small thing to be bothered by but I feel it has completely taken away the magic they had to them back in gen2.
That's what the last 3 generations of pokemon have felt to me anyways: the franchise's magic being slowly chipped away, bit by bit, by their overreliance on generational gimmicks as a marketing strategy. Don't get me wrong, I get it, I get that they need to put something new and "cool" into the shelves to attract new kids to the games with the "new shiny toy" effect. That's how these franchises have always worked, after all.
But the essence of pokemon from back then is completely lost to me. Feels like an entirely different series now, specially with the noticeable changes in design philosophy since the introduction of full 3D pokemon models into the core line.
I guess... this probably just means it's time to move on for me.